Starting phenix.real_space_refine on Wed Jul 1 20:45:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vu8_32126/07_2026/7vu8_32126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vu8_32126/07_2026/7vu8_32126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7vu8_32126/07_2026/7vu8_32126.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vu8_32126/07_2026/7vu8_32126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vu8_32126/07_2026/7vu8_32126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vu8_32126/07_2026/7vu8_32126.map" model { file = "/net/cci-nas-00/data/ceres_data/7vu8_32126/07_2026/7vu8_32126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vu8_32126/07_2026/7vu8_32126.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 5 5.16 5 C 914 2.51 5 N 251 2.21 5 O 262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1433 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1411 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'ACK': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.69, per 1000 atoms: 0.48 Number of scatterers: 1433 At special positions: 0 Unit cell: (66.066, 54.054, 48.048, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 5 16.00 P 1 15.00 O 262 8.00 N 251 7.00 C 914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.17 Conformation dependent library (CDL) restraints added in 80.2 milliseconds 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 1 sheets defined 50.6% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'B' and resid 68 through 73 Processing helix chain 'B' and resid 76 through 86 removed outlier: 3.681A pdb=" N LEU B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR B 86 " --> pdb=" O HIS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 129 through 146 removed outlier: 4.028A pdb=" N LEU B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 138 " --> pdb=" O MET B 134 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP B 146 " --> pdb=" O ARG B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 177 removed outlier: 3.683A pdb=" N LYS B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 180 No H-bonds generated for 'chain 'B' and resid 178 through 180' Processing helix chain 'B' and resid 184 through 197 removed outlier: 4.061A pdb=" N LYS B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 227 removed outlier: 3.817A pdb=" N HIS B 224 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 63 through 66 removed outlier: 6.452A pdb=" N PHE B 64 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR B 118 " --> pdb=" O ILE B 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 41 hydrogen bonds defined for protein. 123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.17 Time building geometry restraints manager: 0.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 341 1.33 - 1.45: 326 1.45 - 1.57: 796 1.57 - 1.69: 2 1.69 - 1.81: 7 Bond restraints: 1472 Sorted by residual: bond pdb=" O3P ACK B 301 " pdb=" P ACK B 301 " ideal model delta sigma weight residual 1.588 1.480 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C PHE B 76 " pdb=" O PHE B 76 " ideal model delta sigma weight residual 1.235 1.288 -0.054 1.23e-02 6.61e+03 1.89e+01 bond pdb=" C THR B 77 " pdb=" O THR B 77 " ideal model delta sigma weight residual 1.236 1.284 -0.047 1.25e-02 6.40e+03 1.43e+01 bond pdb=" N ILE B 89 " pdb=" CA ILE B 89 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.15e-02 7.56e+03 1.27e+01 bond pdb=" N THR B 72 " pdb=" CA THR B 72 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.22e-02 6.72e+03 1.06e+01 ... (remaining 1467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 1814 2.12 - 4.24: 161 4.24 - 6.35: 8 6.35 - 8.47: 1 8.47 - 10.59: 3 Bond angle restraints: 1987 Sorted by residual: angle pdb=" N ASP B 198 " pdb=" CA ASP B 198 " pdb=" C ASP B 198 " ideal model delta sigma weight residual 114.56 107.84 6.72 1.27e+00 6.20e-01 2.80e+01 angle pdb=" N TYR B 87 " pdb=" CA TYR B 87 " pdb=" C TYR B 87 " ideal model delta sigma weight residual 113.02 107.90 5.12 1.20e+00 6.94e-01 1.82e+01 angle pdb=" C LEU B 98 " pdb=" CA LEU B 98 " pdb=" CB LEU B 98 " ideal model delta sigma weight residual 117.23 112.07 5.16 1.36e+00 5.41e-01 1.44e+01 angle pdb=" CA VAL B 63 " pdb=" C VAL B 63 " pdb=" O VAL B 63 " ideal model delta sigma weight residual 121.49 117.79 3.70 1.01e+00 9.80e-01 1.34e+01 angle pdb=" N ASP B 95 " pdb=" CA ASP B 95 " pdb=" C ASP B 95 " ideal model delta sigma weight residual 114.39 109.10 5.29 1.45e+00 4.76e-01 1.33e+01 ... (remaining 1982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.50: 736 10.50 - 21.01: 81 21.01 - 31.51: 27 31.51 - 42.01: 16 42.01 - 52.51: 5 Dihedral angle restraints: 865 sinusoidal: 368 harmonic: 497 Sorted by residual: dihedral pdb=" N LYS B 227 " pdb=" CA LYS B 227 " pdb=" CB LYS B 227 " pdb=" CG LYS B 227 " ideal model delta sinusoidal sigma weight residual -180.00 -127.49 -52.51 3 1.50e+01 4.44e-03 9.12e+00 dihedral pdb=" N PHE B 79 " pdb=" CA PHE B 79 " pdb=" CB PHE B 79 " pdb=" CG PHE B 79 " ideal model delta sinusoidal sigma weight residual -180.00 -130.34 -49.66 3 1.50e+01 4.44e-03 8.80e+00 dihedral pdb=" CA ARG B 110 " pdb=" CB ARG B 110 " pdb=" CG ARG B 110 " pdb=" CD ARG B 110 " ideal model delta sinusoidal sigma weight residual -180.00 -133.44 -46.56 3 1.50e+01 4.44e-03 8.36e+00 ... (remaining 862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 124 0.047 - 0.094: 51 0.094 - 0.141: 18 0.141 - 0.188: 5 0.188 - 0.236: 6 Chirality restraints: 204 Sorted by residual: chirality pdb=" CA LYS B 100 " pdb=" N LYS B 100 " pdb=" C LYS B 100 " pdb=" CB LYS B 100 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE B 104 " pdb=" CA ILE B 104 " pdb=" CG1 ILE B 104 " pdb=" CG2 ILE B 104 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE B 151 " pdb=" N ILE B 151 " pdb=" C ILE B 151 " pdb=" CB ILE B 151 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 201 not shown) Planarity restraints: 251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 70 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C PRO B 70 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO B 70 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP B 71 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 71 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C ASP B 71 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP B 71 " -0.013 2.00e-02 2.50e+03 pdb=" N THR B 72 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 86 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C TYR B 86 " 0.033 2.00e-02 2.50e+03 pdb=" O TYR B 86 " -0.012 2.00e-02 2.50e+03 pdb=" N TYR B 87 " -0.011 2.00e-02 2.50e+03 ... (remaining 248 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 407 2.83 - 3.34: 1290 3.34 - 3.86: 2123 3.86 - 4.38: 2502 4.38 - 4.90: 3971 Nonbonded interactions: 10293 Sorted by model distance: nonbonded pdb=" OD1 ASP B 182 " pdb=" N GLY B 183 " model vdw 2.308 3.120 nonbonded pdb=" OE2 GLU B 138 " pdb=" NH2 ARG B 141 " model vdw 2.308 3.120 nonbonded pdb=" CD2 LEU B 98 " pdb=" N ARG B 99 " model vdw 2.426 3.540 nonbonded pdb=" NE ARG B 164 " pdb=" O GLY B 197 " model vdw 2.428 3.120 nonbonded pdb=" O ALA B 219 " pdb=" OG SER B 223 " model vdw 2.436 3.040 ... (remaining 10288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.920 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.108 1472 Z= 0.674 Angle : 1.189 10.589 1987 Z= 0.809 Chirality : 0.069 0.236 204 Planarity : 0.005 0.033 251 Dihedral : 11.958 52.515 545 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 4.64 % Allowed : 7.95 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.27 (0.46), residues: 168 helix: -3.13 (0.41), residues: 66 sheet: -5.55 (0.71), residues: 19 loop : -3.25 (0.52), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 68 TYR 0.007 0.001 TYR B 87 PHE 0.007 0.001 PHE B 83 TRP 0.006 0.001 TRP B 202 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00945 / 0.67 ( 1472) covalent geometry : angle 1.18944 / 0.81 ( 1987) hydrogen bonds : bond 0.32582 / 20.70 ( 41) hydrogen bonds : angle 10.34552 / 6.62 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.067 Fit side-chains REVERT: B 72 THR cc_start: 0.8244 (p) cc_final: 0.8016 (p) REVERT: B 86 TYR cc_start: 0.7722 (m-80) cc_final: 0.7138 (t80) REVERT: B 119 VAL cc_start: 0.8934 (t) cc_final: 0.8672 (m) outliers start: 7 outliers final: 0 residues processed: 49 average time/residue: 0.4116 time to fit residues: 20.5514 Evaluate side-chains 24 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.143376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.114929 restraints weight = 2393.148| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 4.76 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1472 Z= 0.127 Angle : 0.588 5.365 1987 Z= 0.300 Chirality : 0.046 0.129 204 Planarity : 0.003 0.023 251 Dihedral : 3.995 11.822 188 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 7.28 % Allowed : 18.54 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.58), residues: 168 helix: -0.85 (0.56), residues: 70 sheet: -4.76 (0.87), residues: 19 loop : -2.56 (0.63), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 164 TYR 0.010 0.001 TYR B 156 PHE 0.012 0.001 PHE B 92 TRP 0.011 0.001 TRP B 189 HIS 0.003 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 1472) covalent geometry : angle 0.58808 / 0.30 ( 1987) hydrogen bonds : bond 0.03669 / 2.19 ( 41) hydrogen bonds : angle 5.08728 / 3.10 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.058 Fit side-chains REVERT: B 86 TYR cc_start: 0.7786 (m-80) cc_final: 0.7166 (t80) outliers start: 11 outliers final: 5 residues processed: 33 average time/residue: 0.3428 time to fit residues: 11.6004 Evaluate side-chains 28 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 218 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 3 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 203 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.138493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.110488 restraints weight = 2496.224| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 4.88 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 1472 Z= 0.180 Angle : 0.633 8.902 1987 Z= 0.324 Chirality : 0.049 0.133 204 Planarity : 0.005 0.059 251 Dihedral : 4.309 12.299 188 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 10.60 % Allowed : 17.22 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.63), residues: 168 helix: 0.09 (0.64), residues: 70 sheet: -4.78 (0.85), residues: 19 loop : -2.42 (0.62), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 93 TYR 0.011 0.002 TYR B 118 PHE 0.012 0.002 PHE B 76 TRP 0.008 0.001 TRP B 202 HIS 0.004 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 ( 1472) covalent geometry : angle 0.63309 / 0.32 ( 1987) hydrogen bonds : bond 0.03784 / 2.23 ( 41) hydrogen bonds : angle 5.01260 / 3.11 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 22 time to evaluate : 0.070 Fit side-chains REVERT: B 86 TYR cc_start: 0.7760 (m-80) cc_final: 0.7042 (t80) outliers start: 16 outliers final: 10 residues processed: 33 average time/residue: 0.2803 time to fit residues: 9.5401 Evaluate side-chains 29 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.141006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.113557 restraints weight = 2475.285| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 4.82 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1472 Z= 0.104 Angle : 0.575 7.798 1987 Z= 0.277 Chirality : 0.044 0.131 204 Planarity : 0.004 0.049 251 Dihedral : 3.942 10.995 188 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 6.62 % Allowed : 22.52 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.64), residues: 168 helix: 0.60 (0.66), residues: 72 sheet: -4.39 (0.93), residues: 19 loop : -2.43 (0.61), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 93 TYR 0.005 0.001 TYR B 156 PHE 0.005 0.001 PHE B 67 TRP 0.006 0.001 TRP B 202 HIS 0.002 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.10 ( 1472) covalent geometry : angle 0.57486 / 0.28 ( 1987) hydrogen bonds : bond 0.02833 / 1.68 ( 41) hydrogen bonds : angle 4.24597 / 2.60 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 0.046 Fit side-chains REVERT: B 86 TYR cc_start: 0.7663 (m-80) cc_final: 0.6973 (t80) REVERT: B 129 SER cc_start: 0.8339 (OUTLIER) cc_final: 0.7935 (m) REVERT: B 130 LYS cc_start: 0.2123 (pttt) cc_final: 0.1334 (mttp) REVERT: B 226 SER cc_start: 0.4443 (t) cc_final: 0.3922 (m) outliers start: 10 outliers final: 5 residues processed: 30 average time/residue: 0.2896 time to fit residues: 8.9211 Evaluate side-chains 27 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 21 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 12 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.141384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.114242 restraints weight = 2374.664| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 4.68 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1472 Z= 0.107 Angle : 0.547 6.824 1987 Z= 0.271 Chirality : 0.045 0.132 204 Planarity : 0.004 0.044 251 Dihedral : 3.842 10.293 188 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 8.61 % Allowed : 19.21 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.63), residues: 168 helix: 0.57 (0.65), residues: 74 sheet: -4.23 (0.95), residues: 19 loop : -2.59 (0.57), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 93 TYR 0.005 0.001 TYR B 118 PHE 0.005 0.001 PHE B 76 TRP 0.006 0.001 TRP B 202 HIS 0.002 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 1472) covalent geometry : angle 0.54651 / 0.27 ( 1987) hydrogen bonds : bond 0.02902 / 1.64 ( 41) hydrogen bonds : angle 4.39590 / 2.81 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 22 time to evaluate : 0.059 Fit side-chains REVERT: B 86 TYR cc_start: 0.7620 (m-80) cc_final: 0.6900 (t80) REVERT: B 130 LYS cc_start: 0.2254 (pttt) cc_final: 0.1535 (mttp) REVERT: B 150 ILE cc_start: 0.8957 (pt) cc_final: 0.8560 (pp) REVERT: B 226 SER cc_start: 0.4474 (t) cc_final: 0.3933 (m) outliers start: 13 outliers final: 6 residues processed: 32 average time/residue: 0.3176 time to fit residues: 10.4169 Evaluate side-chains 25 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 5 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.140890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.113739 restraints weight = 2401.964| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 4.75 r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 1472 Z= 0.199 Angle : 0.641 7.947 1987 Z= 0.321 Chirality : 0.048 0.136 204 Planarity : 0.005 0.044 251 Dihedral : 4.305 11.755 188 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 7.28 % Allowed : 21.85 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.63), residues: 168 helix: 0.76 (0.65), residues: 72 sheet: -4.67 (0.83), residues: 19 loop : -2.49 (0.58), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 93 TYR 0.011 0.002 TYR B 118 PHE 0.008 0.001 PHE B 67 TRP 0.008 0.001 TRP B 202 HIS 0.005 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 ( 1472) covalent geometry : angle 0.64113 / 0.32 ( 1987) hydrogen bonds : bond 0.03556 / 2.09 ( 41) hydrogen bonds : angle 4.60225 / 2.87 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.058 Fit side-chains REVERT: B 86 TYR cc_start: 0.7572 (m-80) cc_final: 0.6873 (t80) REVERT: B 130 LYS cc_start: 0.2275 (pttt) cc_final: 0.1587 (mttp) REVERT: B 226 SER cc_start: 0.4659 (t) cc_final: 0.4092 (m) outliers start: 11 outliers final: 10 residues processed: 30 average time/residue: 0.2961 time to fit residues: 9.1563 Evaluate side-chains 30 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 20 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 0 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.145179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.116996 restraints weight = 2382.834| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 4.80 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1472 Z= 0.092 Angle : 0.545 6.959 1987 Z= 0.260 Chirality : 0.044 0.130 204 Planarity : 0.004 0.040 251 Dihedral : 3.799 10.811 188 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.30 % Allowed : 23.18 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.64), residues: 168 helix: 1.03 (0.66), residues: 74 sheet: -4.18 (0.94), residues: 19 loop : -2.58 (0.57), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 93 TYR 0.006 0.001 TYR B 156 PHE 0.005 0.001 PHE B 67 TRP 0.006 0.001 TRP B 202 HIS 0.001 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.09 ( 1472) covalent geometry : angle 0.54526 / 0.26 ( 1987) hydrogen bonds : bond 0.02459 / 1.42 ( 41) hydrogen bonds : angle 3.96368 / 2.43 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.062 Fit side-chains REVERT: B 86 TYR cc_start: 0.7567 (m-80) cc_final: 0.6782 (t80) REVERT: B 130 LYS cc_start: 0.2145 (OUTLIER) cc_final: 0.1429 (mttp) REVERT: B 150 ILE cc_start: 0.8926 (pt) cc_final: 0.8519 (pp) REVERT: B 226 SER cc_start: 0.4390 (t) cc_final: 0.3894 (m) outliers start: 8 outliers final: 6 residues processed: 26 average time/residue: 0.3874 time to fit residues: 10.3247 Evaluate side-chains 25 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 169 CYS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 0.0980 chunk 3 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.147493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.119034 restraints weight = 2345.895| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 4.78 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1472 Z= 0.077 Angle : 0.510 5.948 1987 Z= 0.243 Chirality : 0.043 0.130 204 Planarity : 0.003 0.039 251 Dihedral : 3.464 10.087 188 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.97 % Allowed : 26.49 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.64), residues: 168 helix: 0.84 (0.64), residues: 80 sheet: -3.79 (1.01), residues: 19 loop : -2.40 (0.58), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 93 TYR 0.006 0.001 TYR B 156 PHE 0.003 0.001 PHE B 64 TRP 0.006 0.001 TRP B 202 HIS 0.001 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00178 / 0.08 ( 1472) covalent geometry : angle 0.50985 / 0.24 ( 1987) hydrogen bonds : bond 0.02028 / 1.15 ( 41) hydrogen bonds : angle 3.75388 / 2.29 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.058 Fit side-chains REVERT: B 86 TYR cc_start: 0.7529 (m-80) cc_final: 0.6762 (t80) REVERT: B 130 LYS cc_start: 0.2080 (pttt) cc_final: 0.1295 (mttp) REVERT: B 134 MET cc_start: 0.7295 (ptm) cc_final: 0.7016 (ptp) REVERT: B 150 ILE cc_start: 0.8905 (pt) cc_final: 0.8529 (pp) REVERT: B 209 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8060 (mp0) REVERT: B 226 SER cc_start: 0.4423 (t) cc_final: 0.3933 (m) outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 0.2911 time to fit residues: 7.5116 Evaluate side-chains 22 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 5 optimal weight: 0.0270 overall best weight: 1.0840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.146422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.118750 restraints weight = 2320.763| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 4.73 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1472 Z= 0.081 Angle : 0.503 5.686 1987 Z= 0.242 Chirality : 0.043 0.129 204 Planarity : 0.005 0.072 251 Dihedral : 3.438 9.935 188 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.97 % Allowed : 27.81 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.65), residues: 168 helix: 1.44 (0.65), residues: 74 sheet: -3.65 (1.00), residues: 19 loop : -2.36 (0.57), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 93 TYR 0.023 0.001 TYR B 81 PHE 0.003 0.001 PHE B 67 TRP 0.005 0.001 TRP B 202 HIS 0.002 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00186 / 0.08 ( 1472) covalent geometry : angle 0.50285 / 0.24 ( 1987) hydrogen bonds : bond 0.02061 / 1.17 ( 41) hydrogen bonds : angle 3.71820 / 2.26 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 18 time to evaluate : 0.056 Fit side-chains REVERT: B 86 TYR cc_start: 0.7598 (m-80) cc_final: 0.6798 (t80) REVERT: B 130 LYS cc_start: 0.2185 (pttt) cc_final: 0.1412 (mttp) REVERT: B 134 MET cc_start: 0.7253 (ptm) cc_final: 0.6947 (ptp) REVERT: B 150 ILE cc_start: 0.8886 (pt) cc_final: 0.8500 (pp) REVERT: B 209 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8066 (mp0) REVERT: B 226 SER cc_start: 0.4472 (t) cc_final: 0.3964 (m) outliers start: 6 outliers final: 5 residues processed: 23 average time/residue: 0.2989 time to fit residues: 7.0798 Evaluate side-chains 23 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 18 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.147506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.119673 restraints weight = 2305.805| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 4.73 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 1472 Z= 0.094 Angle : 0.540 5.520 1987 Z= 0.267 Chirality : 0.044 0.130 204 Planarity : 0.005 0.071 251 Dihedral : 3.416 9.607 188 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.99 % Allowed : 28.48 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.64), residues: 168 helix: 0.86 (0.62), residues: 80 sheet: -3.54 (0.98), residues: 19 loop : -2.28 (0.61), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 149 TYR 0.020 0.001 TYR B 81 PHE 0.005 0.001 PHE B 64 TRP 0.004 0.001 TRP B 202 HIS 0.001 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.09 ( 1472) covalent geometry : angle 0.54024 / 0.27 ( 1987) hydrogen bonds : bond 0.02841 / 1.55 ( 41) hydrogen bonds : angle 4.19133 / 2.79 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 19 time to evaluate : 0.062 Fit side-chains REVERT: B 86 TYR cc_start: 0.7591 (m-80) cc_final: 0.6806 (t80) REVERT: B 130 LYS cc_start: 0.2178 (pttt) cc_final: 0.1438 (mttp) REVERT: B 134 MET cc_start: 0.7092 (ptm) cc_final: 0.6830 (ptp) REVERT: B 150 ILE cc_start: 0.8844 (pt) cc_final: 0.8436 (pp) REVERT: B 209 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8080 (mp0) REVERT: B 226 SER cc_start: 0.4600 (t) cc_final: 0.4067 (m) outliers start: 3 outliers final: 3 residues processed: 21 average time/residue: 0.3370 time to fit residues: 7.2791 Evaluate side-chains 20 residues out of total 151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 199 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 17 random chunks: chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.148342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.120537 restraints weight = 2336.328| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 4.76 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 1472 Z= 0.094 Angle : 0.566 5.888 1987 Z= 0.278 Chirality : 0.044 0.130 204 Planarity : 0.005 0.070 251 Dihedral : 3.471 10.046 188 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.99 % Allowed : 29.14 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.64), residues: 168 helix: 0.91 (0.63), residues: 80 sheet: -2.98 (1.05), residues: 19 loop : -2.25 (0.61), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 68 TYR 0.019 0.001 TYR B 81 PHE 0.005 0.001 PHE B 64 TRP 0.004 0.001 TRP B 202 HIS 0.001 0.000 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.09 ( 1472) covalent geometry : angle 0.56561 / 0.28 ( 1987) hydrogen bonds : bond 0.02435 / 1.32 ( 41) hydrogen bonds : angle 4.09303 / 2.73 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 650.76 seconds wall clock time: 12 minutes 2.90 seconds (722.90 seconds total)